Topics in Current Genetics – serie

Yeasts have a longstanding history as domesticated organisms. The brewing of beer and wine and the leavening of bread dough are well-known artisanal applications of yeast. These early examples of yeast biotechnology have clearly contributed to the acceptance of yeasts, both as biotechnological workhorses and as model systems for the detailed understanding of eukaryotic molecular cell biology and genetics. In recent years, new yeast species have proven their value and novel biotechnological applications have emerged. This book compiles the multi-faceted genetic repertoire of several yeasts relevant to modern biotechnology, and describes their utilization in research and application in the light of their genetic make-up and physiological characteristics. Moreover, the book presents a thorough overview of a wide array of methodologies from classical genetics to modern genomics technologies that have been and are being used in functional analysis of yeasts.

Aging is the progressive decline in biological functions over time. This decline targets macromolecules, cells, tissues and, as a consequence, whole organisms. Despite considerable progress in the development of testable hypothesis concerning aging in an evolutionary context, a unifying theory of the molecular/physiological mechanistic causes of aging has not been reached. In fact, is it not clear to what extent aging is a programmed or stochastic process. This book takes the reader from unicellular bacterial deterioration via senescence in fungi and worms to aging in rodents and humans, allowing a comparative view on similarities and differences in different genetic model systems. The different model systems are scrutinized in the light of contemporary aging hypothesis, such as the free radical and genomic instability theories.

Environmental stresses represent the most limiting factors for agricultural productivity. Apart from biotic stress caused by plant pathogens, there are a number of abiotic stresses such as extremes in temperature, drought, salinity, heavy metals and radiation which all have detrimental effects on plant growth and yield. However, certain plant species and ecotypes have developed various mechanisms to adapt to such stress conditions. Recent advances in the understanding of these abiotic stress responses provided the impetus for compiling up-to-date reviews discussing all relevant topics in abiotic stress signaling of plants in a single volume. Topical reviews were prepared by selected experts and contain an introduction, discussion of the state of the art and important future tasks of the particular fields.

This book provides an up-to-date and comprehensive overview of protein phosphatase research, a rapidly evolving field with increasing importance in our understanding of the molecular basis of cell biology and of pathological processes. The book covers dephosphorylation processes involving serine/threonine, as well as tyrosine and histidine residues, and aims to be a useful resource for both the advanced reader as well as the newcomer to the field. It is also valuable for those working in the pharmaceutical and Biotech industries.

The series of review articles presented in this book summarizes the recent state of the art in lipid research in a comprehensive way. The authors provide a general overview of this field and draw the readers attention to the most recent investigation. Biochemical, cell biological and biophysical aspects of the four major groups of lipids in eukaryotic cells, namely glycerophospholipids, sterols, sphingolipids and storage lipids, are reported and discussed. The experimental systems addressed are mammalian, plant and yeast cells as the most prominent and currently best studied systems in lipid biochemistry, cell and molecular biology.

Cells of all living organisms have the ability to respond to altered nutritional conditions. They have developed mechanisms to sense nutrient availability and to produce appropriate responses, which involve changes in gene expression and the production or degradation of certain enzymes and other proteins. In recent years, the understanding of nutrient-induced signal transduction has greatly advanced and the emerging picture is that nutrient signalling mechanisms evolved early in evolution. This book provides a detailed presentation and comparison of the key nutritional regulatory mechanisms in lower as well as higher eukaryotes, written by recognised experts in this expanding field.

Mitochondria are complex organelles, possessing a double-membrane and even their own genome, the mtDNA. They play a pivotal role in cellular metabolism, respiration, and production of ATP essential for the normal function of all human organ systems. It is not surprising, therefore, that genetic defects of mitochondrial functions cause a wide spectrum of human diseases. This book provides the first modern and truly comprehensive coverage of the biochemistry, genetics, and pathology of mitochondria in different organisms. It particularly focuses on the recent advances in our understanding of basic mitochondrial research to the consequences of dysfunction at the molecular level. The 13 contributions written by leading researchers in the field include topics such as: mitochondrial genome evolution and mtDNA stability, mitochondrial biogenesis and protein quality control, mitochondrial morphology, assembly and function of the mitochondrial energy generation apparatus and mitochondrial metabolic pathways. These are particularly oriented to link in these various mitochondrial pathways to the clinical consequences of their dysfunctions.

All living cells are strictly separated from their surroundings by a membranous lipid bilayer. Into these membranes a variety of transport proteins are embedded that ensure the uptake and secretion of various molecules and ions. In order to respond properly to a changing nutrient supply or demand, as well as to external stress factors, cells must be able to adapt both amount and activity of the corresponding transporters. This book provides readers with state-of-the-art knowledge on the various regulatory mechanisms that control transmembrane transporter expression, activity and their subcellular localisation.

One of the challenges faced by every cell as well as by whole organisms is to maintain appropriate concentrations of essential nutrient metals while excluding nonessential toxic metals. Toward that end, all organisms have developed mechanisms for metal homeostasis and detoxification to maintain metal levels within physiological limits. This book brings together current knowledge of the molecular basis of metal homeostasis and detoxification in various eukaryotic model systems, including yeasts, plants, and mammals. It focuses on the cellular systems controlling metal transport, intracellular distribution, and immobilization as well as on systems regulating metal-dependent transcription. In addition to environmental aspects (including phytoremediation), the book treats the pathophysiology of metal deficiency and overload in relation to disease.

This book deals with the molecular mechanisms of membrane trafficking, a central eukaryotic cell biological process. In the post-genomic era many essential molecules involved in intracellular membrane/protein transport are emerging. A huge task now is to compile the molecular networks that govern these processes. Understanding of regulatory processes and participating molecules are likely to reveal global cellular regulatory circuits that couple membrane trafficking with other cellular functions. Such cell biological features are only starting to emerge. This book puts special emphasis on such mechanisms and processes. The contents discusses the role of coat proteins, tethering complexes, small rab GTPases, Sec1-family proteins and SNARE molecule phosphorylation in exocytosis, endocytosis and membrane fusion. In addition, the role of lipids in vesicle formation and membrane fusion, and some specialized cell biological denovo membrane generation processes are discussed.

The wealth of genomic and post-genomic data needs to be structured so that the understanding of complex cellular processes can be achieved by creating computational models able to describe and predict phenotypes at the cell or organism level in health and disease. This book provides a detailed presentation of systems biology studies that are paving the way towards the above-mentioned goal and discusses the most efficient experimental and computational strategies for this purpose. The potential benefits for bioindustry, in particular the discovery of new drugs and better management, are also presented.

Since the initial establishment of Robert Koch’s postulates in the nineteenth century, microbial protein toxins have been recognized as a major factor of bacterial and fungal virulence. An increasing number of proteins produced and secreted by various bacteria, yeasts and plants are extremely toxic and most of them developed remarkably "intelligent" strategies to enter, to penetrate and to finally kill a eukaryotic target cell by modifying or blocking essential cellular components. This book describes the strategies employed by protein toxins to render their pro- and eukaryotic producers a selective growth advantage over competitors. In providing an up-to-date overview on the mode of protein toxin actions, it accommodates biomedically and biologically relevant toxin model systems. As a result, it significantly broadens our perspective on biochemical architecture and molecular ploy behind the lethal principles of pro- and eukaryotic toxins.

Naturally occurring RNA always contains numerous biochemically altered nucleotides. They are formed by enzymatic modification of the primary transcripts during the complex RNA maturation process designated RNA modification. A large number of enzymes catalyzing the formation of these modified nucleosides or converting one canonical base into another at the posttranscriptional level have been studied for many years, but only recently have systematic and comparative studies begun. The functions of individual enzymes and/or the modified/edited nucleosides in RNA, however, have remained largely ignored.This book provides advance information on RNA modification, including the associated editing machinery, while offering the reader some perspective on the significance of such modifications in fine-tuning the structure and functions of mature RNA molecules and hence the ability to influence the efficiency and accuracy of genetic expression. Outstanding scientists who are actively working on RNA modification/editing processes have provided up-to-date information on these intriguing cellular processes that have been generated over the course of millions of years in all living organisms. Each review has been written and illustrated for a large audience of readers, not only specialists in the field, but also for advanced students or researchers who want to learn more about recent progress in RNA modification and editing.

Fungal comparative genomics started in 2000 by the genome sequencing of several yeast species other than the canonical Saccharomyces cerevisiae. Since then, over 30 fungal genome sequences have become available. This set represents a total evolutionary divergence comparable to that between vertebrates and arthropods, but also contains closely related genomes. This volume describes how we can use this set of genomes to trace large and small-scale events in genome evolution, to extract information about highly conserved and less conserved sequence elements, and to develop novel methods in genomics that will have an impact on genomics at large.

Molecular chaperones interact with virtually every newly synthesized protein. Their role is not limited to this, as an increasing number of protein-protein interactions are found to be mediated by molecular chaperones. They reside in large complexes, in every cellular compartment, and to some extent even outside cells. These proteins are of interest to a large number of scientists, not only to those interested in protein biosynthesis, but also in relation to protein transport, organelle biogenesis, and cell stress. Whereas excellent reviews on molecular chaperones are published, they often focus on the latest results without reiterating the basics. The goal of this volume was to assemble a collection of reviews on molecular chaperones that would be both timely and basic, which would make them an excellent entrance for novices into the field and suitable for teaching purposes.

Every cell has developed mechanisms to respond to changes in its environment and to adapt its growth and metabolism to unfavorable conditions. The unicellular eukaryote yeast has long proven as a particularly useful model system for the analysis of cellular stress responses, and the completion of the yeast genome sequence has only added to its powerThis volume comprehensively reviews both the basic features of the yeast genral stress response and the specific adapations to different stress types (nutrient depletion, osmotic and heat shock as well as salt and oxidative stress). It includes the latest findings in the field and discusses the implications for the analysis of stress response mechanisms in higher eukaryotes as well.

Genetic recombination is an important process involved in shaping the genetic make up of progeny. Increasingly, it has become evident that recombination is a DNA repair pathway crucial during DNA replication in vegetatively growing cells. It plays a critical role in preserving the integrity of the genome by mediating the repair of DNA damage, which can occur during normal cellular metabolism as a result of oxidative stress, transcription, replication fork stalling or breakdown, or after the exposure to DNA damaging agents. Until recently, much of our knowledge on the mechanisms of genetic recombination has come from studies of prokaryotic and simple eukaryotic fungal systems. However, these studies have now been significantly extended to mammals, such that a comparative picture of the general factors and mechanisms of genetic recombination is beginning to emerge. Detailed genetic and biochemical studies have led to the isolation and characterization of many of the recombination-repair proteins in E. coli and S. cerevisiae, which in turn has led to the identification of homologues in human cells. The link between recombination defects and recombination proteins in a number of tumors as well as in human hereditary syndromes makes genetic recombination a cellular process of key importance not only in basic biology but also in biomedical studies.

For life to be understood and disease to become manageable, the wealth of postgenomic data now needs to be made dynamic. This development requires systems biology, integrating computational models for cells and organisms in health and disease; quantitative experiments (high-throughput, genome-wide, living cell, in silico); and new concepts and principles concerning interactions. This book defines the new field of systems biology and discusses the most efficient experimental and computational strategies. The benefits for industry, such as the new network-based drug-target design validation, and testing, are also presented.

The metabolome comprises the complete set of metabolites, the non-genetically encoded substrates, intermediates, and products of metabolic pathways, associated with a cell. Given the increasing demand to quantitatively identify the metabolome and understand how trafficking of metabolites through the metabolic network impact cellular behavior, metabolomics has emerged as an important complementary technology to the cell-wide measurements of mRNA, proteins, fluxes, and interactions (e.g., protein-DNA). Metabolomics is already a powerful tool in drug discovery and development and in metabolic engineering. While maintaining these strengths, the field promises to play a heightened role in systems biology research, which is transforming the practice of medicine and our ability to engineer living organisms. This book brings together the latest results in the field of metabolomics. It comprehensively presents the current state of the metabolomics field by underscoring experimental methods, analysis techniques, standardization practices, and advances in specific model systems.As a result, it significantly broadens our perspective on the principles and strategies underpinning this emerging field.

The present book provides a comprehensive overview of our current knowledge on plastid biogenesis, plastid-nuclear communication, and the regulation of plastid gene expression at all levels. It also assesses the state-of-the-art in key technologies, such as proteomics and chloroplast transformation. Written by recognized experts in the field, the book further covers crucial post-translational processes in plastid biogenesis and function, including protein processing.

To maximize the probability of survival, cells need to coordinate their intracellular activities in response to changes in the extracellular environment. MAP kinase cascades play an important role in the transduction of signals inside eukaryotic cells. In particular, stress stimuli result in the rapid activation of a highly conserved group of MAP kinases, known as SAPKs (Stress-Activated Protein Kinases). These kinases coordinate the generation of adaptive responses that are essential for cell survival, which include the modulation of several aspects of cell physiology from metabolism to gene expression.In this book, leading researchers in the field discuss the state-of-the-art of many aspects of SAPK signalling in various systems from yeast to mammals. These include various chapters on regulatory mechanisms as well as the contribution of the SAPK signalling pathways to processes such as gene expression, metabolism, cell cycle regulation, immune responses and tumorigenesis.

Yeasts have a longstanding history as domesticated organisms. The brewing of beer and wine and the leavening of bread dough are well-known ‘artisanal’ applications of yeast. These early examples of yeast biotechnology have clearly contributed to the acceptance of yeasts, both as biotechnological workhorses and as model systems for the detailed understanding of eukaryotic molecular cell biology and genetics. In recent years, new yeast species have proven their value and novel biotechnological applications have emerged. This book compiles the multi-faceted genetic repertoire of several yeasts relevant to modern biotechnology, and describes their utilization in research and application in the light of their genetic make-up and physiological characteristics. Moreover, the book presents a thorough overview of a wide array of methodologies from classical genetics to modern genomics technologies that have been and are being used in functional analysis of yeasts.

Aging is the progressive decline in biological functions over time. This decline targets macromolecules, cells, tissues and, as a consequence, whole organisms. Despite considerable progress in the development of testable hypothesis concerning aging in an evolutionary context, a unifying theory of the molecular/physiological mechanistic causes of aging has not been reached. In fact, is it not clear to what extent aging is a programmed or stochastic process. This book takes the reader from unicellular bacterial deterioration via senescence in fungi and worms to aging in rodents and humans, allowing a comparative view on similarities and differences in different genetic model systems. The different model systems are scrutinized in the light of contemporary aging hypothesis, such as the free radical and genomic instability theories.

Recent advances in the understanding of these abiotic stress responses provided the impetus for compiling up-to-date reviews discussing all relevant topics in abiotic stress signaling of plants in a single volume.

This book provides an up-to-date and comprehensive overview of protein phosphatase research, a rapidly evolving field with increasing importance in our understanding of the molecular basis of cell biology and of pathological processes. The book covers dephosphorylation processes involving serine/threonine, as well as tyrosine and histidine residues, and aims to be a useful resource for both the advanced reader as well as the newcomer to the field. It is also valuable for those working in the pharmaceutical and Biotech industries.

The series of review articles presented in this book summarizes the recent state of the art in lipid research in a comprehensive way. The authors provide a general overview of this field and draw the reader’s attention to the most recent investigation. Biochemical, cell biological and biophysical aspects of the four major groups of lipids in eukaryotic cells, namely glycerophospholipids, sterols, sphingolipids and storage lipids, are reported and discussed. The experimental systems addressed are mammalian, plant and yeast cells as the most prominent and currently best studied systems in lipid biochemistry, cell and molecular biology.

Mitochondria are complex organelles, possessing a double-membrane and even their own genome, the mtDNA. They play a pivotal role in cellular metabolism, respiration, and production of ATP essential for the normal function of all human organ systems. It is not surprising, therefore, that genetic defects of mitochondrial functions cause a wide spectrum of human diseases. This book provides the first modern and truly comprehensive coverage of the biochemistry, genetics, and pathology of mitochondria in different organisms. It particularly focuses on the recent advances in our understanding of basic mitochondrial research to the consequences of dysfunction at the molecular level. The 13 contributions written by leading researchers in the field include topics such as: mitochondrial genome evolution and mtDNA stability, mitochondrial biogenesis and protein quality control, mitochondrial morphology, assembly and function of the mitochondrial energy generation apparatus and mitochondrial metabolic pathways. These are particularly oriented to link in these various mitochondrial pathways to the clinical consequences of their dysfunctions.

One of the challenges faced by every cell as well as by whole organisms is to maintain appropriate concentrations of essential nutrient metals while excluding nonessential toxic metals. Toward that end, all organisms have developed mechanisms for metal homeostasis and detoxification to maintain metal levels within physiological limits. This book brings together current knowledge of the molecular basis of metal homeostasis and detoxification in various eukaryotic model systems, including yeasts, plants, and mammals. It focuses on the cellular systems controlling metal transport, intracellular distribution, and immobilization as well as on systems regulating metal-dependent transcription. In addition to environmental aspects (including phytoremediation), the book treats the pathophysiology of metal deficiency and overload in relation to disease.

This book deals with the molecular mechanisms of membrane trafficking, a central eukaryotic cell biological process. In the post-genomic era many essential molecules involved in intracellular membrane/protein transport are emerging. A huge task now is to compile the molecular networks that govern these processes. Understanding of regulatory processes and participating molecules are likely to reveal global cellular regulatory circuits that couple membrane trafficking with other cellular functions. Such cell biological features are only starting to emerge. This book puts special emphasis on such mechanisms and processes. The contents discusses the role of coat proteins, tethering complexes, small rab GTPases, Sec1-family proteins and SNARE molecule phosphorylation in exocytosis, endocytosis and membrane fusion. In addition, the role of lipids in vesicle formation and membrane fusion, and some specialized cell biological denovo membrane generation processes are discussed.